Disable all but one layer in the autocad file. Make sure that the visible layer is selected.

Use the Region command on the entire layer.

Use the Union command on the entire layer.

Use the Explode command on the entire layer. You will likely have to do this several times, until autocad tells you that the number of objects selected is the same as the number of objects that it couldn't explode.

Use the Pedit command.

Choose Multiple.

Select the entire layer.

Choose 'Yes' to convert lines to polylines.

Choose Join.

Enter a fuzz distance of 0.

Hit escape so as not to repeat the process.

Repeat the process for all layers.

Copy the layers independently, and paste them into the template file. The push down layers should be placed in the boxed regions (top right and bottom left), and the fluid layers in the non-boxed regions (top right and bottom left).

Layers that will be made out of thick PDMS need to be expanded by 1.5%.